...They have had it for 2.5 weeks and just advised that the whole rear abs assembly needs to be replaced...
Umm, there is no 'whole rear ABS assembly' unless they are referring to the ABS metering block and pump motor. There is a rear wheel caliper which isn't ABS, it's just a caliper, there are pads, an ABS wheel speed sensor which will light the ABS Trouble light if something is wrong, plus, the sensor does nothing but supply a signal to the ABS ECU (computer) and there is the brake fluid hose that connects to the ABS metering block. The only thing that is ABS is the pump motor and metering block that meters brake fluid pressure or simply passes the brake fluid through to the rear brake caliper.
There have been a couple of instances reported here in the Forum (IIRC) in which the ABS metering block didn't let the pressure release. They bypassed the metering block and things worked normally. It can ever so rarely happen that the inside of the brake hose cracks and lets a little rubber flap obstruct brake fluid movement.
Before going the 'whole rear ABS assembly' route, be sure that the rear axle is assembled correctly, Check that the ABS sensor housing has the tab & slot aligned, the thick washer is in the correct location and (don't laugh, this happens a lot on the rear wheel) be sure the brake pads are on each side of the disk because sometimes due to assembly glitches both pads end up on one side of the disk. As Walter mentions, check the caliper, pistons & seals.
Based on what is being reported about the
mechanics monkeys it may be time to look for a better shop, sometimes it's worth spending the money. Brakes R Important. Texas is a big state, there should be a better shop someplace. The brakes on an FJR should not be a problem or a factor in keeping and riding the bike for a very long time. If it turns out the whole metering block needs to be replaced $2k isn't wildly out of the ball park. For some reason, the ABS metering block and ABS pump aren't usually available through parts shops, only dealers. It's almost like it's complicated and they would like to have a TRAINED professional do the work.
Edited to add: I'm away from my computer with the FSM, but there is a proportioning valve for the linked brakes too. This shouldn't be related, but it is in the brake system.
Edited 2 add: A competent mechanic can also look at the error log in the ABS ECU and see if any codes have been set.